A simple ruby parser for FCS-formatted flow cytometry data files. Supports writing of data and metadata to human-readable delimited text files or use as a library for further data analysis in ruby.

Requires a ruby interpreter (e.g. [http://ruby-lang.org]) with rubygems installed (this is installed by default for recent versions). Tested only on ruby versions 1.8.7 and 1.9.3.

For information on the default output formats see [output_formats Output Formats]

Currently processes v3.x FCS files only, and is limited at the moment to those with the data section in list mode and with floating point (single- or double-precision) data.

Full YARD api docs are available in the git repository. [http://fcsparse.googlecode.com/git/doc/index.html API Documentation Link].

To install as a ruby gem, run at the command line:

gem install fcsparse

(The gem can also be downloaded from [https://rubygems.org/gems/fcsparse].)

To run from the command line, install the gem, and run from the command line:

fcsparse /path/to/mydata.fcs

where /path/to/mydata.fcs is the full path to the file you want to process.

To process a file into human-readable comma-delimited data from ruby code (require 'rubygems' first for ruby 1.8):

require 'fcsparse'

FCSParse.process_file(filename, include_header_row)

where filename is the name (with path) to your FCS-formatted file, and include_header_row is an optional boolean parameter that specifies whether to write a title for each column in the output file.